Numbering of atoms

User 1fd6ed44b6

06-08-2010 11:39:13

i am using marvin 5.3.4. i am having trouble with atom numbering , for subsquent calculation of RMSD with the pdb structure.

i wish to know how to reorder the default atom numbering??

pleaseeeeeeee help, i have a  submission to make.


ChemAxon 40e8f9506d

06-08-2010 12:23:01

You can use the  manual mapping function:

-move the mouse over any atom

-type m and the number you wish to add to the atom

-repeat this 2 steps over every atom you'd like to number


To remove atom map, type: m0

User 870ab5b546

18-08-2010 01:46:24

If you mean the inherent atom numbering rather than atom mapping, the atoms are numbered according to their order of appearance in the code (SMILES, MOL, MRV) that describes the drawing.  To renumber the atoms, you need to rearrange the order of atoms (taking care to make sure the bonds stay in the same place).  

Alternatively, you can redraw the molecule; Marvin will number atoms according to the sequence in which you place them on the canvas.

ChemAxon 990acf0dec

18-08-2010 12:21:34

Yes, this is also a solution; thank you Bob.